3D Printing of Molecular Models

Adam Gardner

Arthur Olson

Abstract

Physical molecular models have played a valuable role in our understanding of the
invisible nano-scale world. We discuss 3D printing and its use in producing
models of the molecules of life. Complex biomolecular models, produced from 3D
printed parts, can demonstrate characteristics of molecular structure and
function, such as viral self-assembly, protein folding, and DNA structure.
Advances in computer and user interface technology have enabled physical
molecular models to combine with augmented reality to bridge the physical with
the computational world.

Introduction

Physical models have had a long and important role in exploring and communicating
scientific and medical concepts and structures. One of the earliest physical
scientific visualizations was the orrery, a mechanical model of the solar system,
which first appeared in Greece around 150 BC. Early anatomical models, such as those
made from papier-mâché were developed in the early-19th century. And,
the earliest molecular models were those produced in the mid-19th century by
chemists such as Hoffman and Kekule to visualize the nature of chemical composition.
These models brought abstract or unseen structures into the context of human
experience.

Physical models convey spatial relationships and mechanisms in ways that images alone
cannot. They engage perceptual and cognitive processes that go beyond the visual,
and bring a sense of reality and natural interaction into the process of exploration
and understanding. In the context of molecular science, they create a human-scale,
tangible representation to objects that are too small to be directly perceived.
Physical molecular models can also serve as “analogue computers,”
where the spatial relationships between the components involved in complex molecular
interactions can be explored and manipulated. The prime example of this utility was
in the discovery of the structure of DNA. Watson and Crick manipulated models of the
nucleotide bases, whose structures and dimensions were already known from chemistry,
to develop the double helical model of base-pair complementarity, that explained the
molecular mechanism of genetic inheritance, underlying all of biology.

Throughout the first half of the 20th century, physical molecular models were
ubiquitous in chemical laboratories and educational institutions. The advent of
interactive computer graphics in the 1960’s and 70’s eventually
replaced such models with images on a computer screen. The power and unlimited
variability of a computer model had significant advantages over the fixed nature of
a physical model. This was especially true for complex biological molecules, which
were very time consuming and difficult to accurately build as physical models. On
the other hand, the real-world physical models had characteristics, as mentioned
above, that provided advantages that the computer images lacked. The advent of
computer auto-fabrication, now referred to as solid or 3D printing, provided an
automated way to produce physical objects from computer data, and opened up the
possibility of having highly accurate, material visualizations of complex molecules
and their assemblies. Here we discuss the nature of 3D printed molecular models, how
they are produced, and what they can provide for visualization and
communication.

Methods

3D Printer Basics

3D printing is an additive manufacturing process in which an object is produced
layer by layer from a digital geometric description of a model. The computer
model must describe the boundaries of the object in such a way that there is an
unambiguous distinction between what is inside and what is outside of the
object. This computer model is sliced into planar sections, so that a 3D printer
can reconstruct the model by depositing or fusing material for each successive
section. While there are a growing number of different types of 3D printers,
with a wide variety of mechanisms and materials, currently all 3D printers
operate in this way. The fact that the output from a 3D printer is a physical
object, dictates that there are both material and physical constraints inherent
in the production and subsequent use of the printed object. These constraints
depend upon the nature of the 3D printer and the material used. The
characteristics of the printing process and output model, such as speed of
production, strength, precision, durability, and color are important to take
into consideration in the conception, design, and production of any 3D printed
model.

The most common 3D printers on the market today can be classified by the kind of
material feedstock that they require. The first 3D printers to come on the
market used photo activated liquid resins. These resins solidify when exposed to
light of a specific wavelength. An object can be “printed” by a
laser, scanning successive slices of the object on a platform that descends,
step-by-step in the liquid resin. After the final “top” slice is
scanned, the platform rises out of the surrounding liquid resin, exposing the
solidified object. Two issues that are common to many 3D printing techniques
arise in this process. First, as an arbitrarily shaped object is being printed
layer-by-layer, there may be parts of the object that have nothing below it in
the previously printed layer. Thus, there must be some support structure
designed into the process that is built along with the object being printed. In
these resin-based printers, the support structure is printed from the same
resin, but designed to be broken away after the printing is finished. Secondly,
many of the 3D printing methods require some “finishing” or
post-processing. In the case of the early resin printers, ultraviolet light
hardening or curing was required prior to the manual removal of the supporting
structure. The finished product from the resin-based printer has the appearance
of a piece of transparent amber. Little or no color variation could be attained
in these early resin-based printers. Today there are more advanced resin-based
printers that can deposit multiple, different, photosensitive materials onto
each section, enabling a mixture of material characteristics and expanded color
variation.

Another type of 3D printer uses powder or fine granules of material. The first
commercially available, full color, 3D printers use gypsum (plaster of Paris)
powder. Color binder “inks” are applied with inkjet printer heads
onto each successive layer of the powder after it is spread on a descending
platform. For full color, four print heads with cyan, yellow, magenta and clear
binder are used. The white unbound powder remains loose and serves as a support
for subsequently built layers of the object. Thus, when the printing is
finished, the printed object lays buried in the loose powder and it must be
carefully excavated and any remaining loose powder must be removed. Since the
inkjet print heads cannot utilize strong glues, the object is porous and
fragile. It must be carefully removed from the printer to be post-processed in
order to strengthen it by infusing a stronger binder, such as wax or superglue.
Other granule-based printers use laser sintering to heat fuse the object layer
by layer. The sintering granules can range from nylon to metal. These objects
are quite strong when they are removed from the loose powder, but they are
monochrome, and if color is desired, it must be applied afterward –
typically by dyeing or hand painting.

Another popular class of commercially available 3D printers uses a process known
as fused deposition modeling (FDM). These printers utilize plastic filament
feedstock which is fed from a reel through a computer controlled XY linear axes
moving heated nozzle and extruded as a fine thread scanning sections of the
model, layer by layer onto a platform that moves in Z axis. Like the resin
printers, support material must also be deposited in each layer to underpin any
model overhangs in the layers that follow. The feedstock is typically a single
color, but some printers come with multiple heads for multiple materials,
including different colors or soluble support material.

The cost of 3D printers varies widely, depending on the nature of the printing
mechanism, its reliability and precision, as well as the size of the
printer’s build volume and material characteristics of the feedstock.
Multi-material photo activated resin printers and laser sintering printers can
cost upward of hundreds of thousands of dollars, while the extruded plastic
printers can be had for as little as $1000, and are trending toward becoming
consumer “appliances.” While owning a 3D printer may now be widely
achievable, there also exists an increasing number of 3D printing services that
provide greater capabilities and wider material choices that are not otherwise
available to the consumer. The cost of a 3D printed object is typically a
function of the time on the printer, the cost of the feedstock materials, as
determined by the size of the printed object, and by the human time that is
required in the setup and post processing of the piece.

Table 1

Some commercially available 3D printers (Consumer and Professional)

Consumer (Hobbyist)

Printer

Manufacturer

Class

Materials

Support

Material Color

Material Cost

Machine Cost

RepRap

Open Source

FDM

Multiple

Plastic Rafting

1 - 3+

Variable

Variable

Makerbot

Makerbot Industries

FDM

PLA, ABS, Flexible

Plastic Rafting Dissolvable Support

1 - 2

Low

$1,375 - 6,499

Form1

FormLabs

Stereo- lithography

Photo Activated Resins

Hanging Support

Clear, White, Grey, Black

Medium

$3,200

CubeX

Stratasys

FDM

ABS

Plastic Rafting

1 - 3

Medium

$2,499 - 3,999

Professional

Dimension

Stratasys

FDM

ABS

Dissolvable Support

1

High

$35,000- 70,000

ProJet (Z Corp)

3D Systems

Plaster

Self-Supporting

Full Color

High

$25,000- 80,000

Objet

Stratasys

Sprayed Photopolymer

Photo Activated Resins

Wax Support

Selected Color

High

$30,000- 150,000

Mcor

Mcor Technologies

Fused Paper

Paper

Self-Supporting

Full Color

Low

$35,000 - 50,000

3D Printing of Molecular Models

Molecules are comprised of atoms, bonded together into a specific connectivity and
3D geometry. Biological molecules, such as proteins, carbohydrates, and nucleic
acids can be comprised of hundreds to thousands of atoms. The principal source
for atomic coordinates of biomolecules is the Protein Data Bank, which currently
holds over 100,000 entries. These entries are in the form of the atomic
coordinates of the molecular structures. As such, they contain only the three
dimensional points in space (the X, Y, Z axes positions) of the atoms and their
chemical types. To turn that information into a buildable 3D object, the first
task is to decide on a representation in which to render the molecular
structure. It should be noted that the molecular images that are rendered on a
computer screen do not necessarily translate well into a solid physical model,
since both the nature of the 3D printer and the geometry and mechanical
characteristics of the real-world model can defeat the change in medium.

Specifying all of the atoms in the molecule as spheres of characteristic atomic
radii – the so-called CPK (Corey-Pauling-Kultun) model – is the simplest
representation, but has some drawbacks, from the 3D printing perspective. Each
sphere is typically represented by a triangular polygonal mesh. Thus, CPK models
of protein structure are comprised of a very large number of polygons, many of
which intersect with each other. This representation can create very large print
files. Additionally, most of these atomic spheres are internal to the protein
and are not visible in the physical model, and the packing of these spheres
leaves numerous small vacant spaces, from which it may be difficult to remove
powder or other support material.

Another popular computer graphic molecular representation is the protein backbone
ribbon model, which shows the molecular “skeleton” or 3D fold.
Since this representation is essentially a meandering curvilinear structure it
may need extra bolstering (e.g. struts). This depends upon the strength and
characteristics of the printing material used, so that the model is robust
enough to build and handle without breakage. Plastic and resin models are more
robust than the full color gypsum-based models for this type of representation.
However, even in plastic, FDM models with long, thin rod-like sections may be
quite weak. Moreover, the orientation of the model in the build can determine
the strength of the finished part – rods printed parallel to the section
direction are much stronger than those aligned perpendicular to it.

The third class of molecular representations depict the molecular surface, or
skin, -- that part of the molecule that can come in contact with the solvent
environment (usually water). Several molecular modeling codes provide for the
calculation of the solvent accessible (or solvent excluded) molecular surface,
which provides an atomic resolution description of such a surface. In addition,
lower resolution molecular surfaces can be used to represent the shape of the
molecule at a user-defined level of detail. They are typically isocontour
surfaces of a volume, derived from Gaussian functions placed at atomic centers.
Molecular surfaces are ideal for representing the shape of large biological
molecules for 3D printing, since they have a lower polygon count and are
typically compact globular structures, needing no additional bolstering for
mechanical strength. Additionally, surface models can be built with hollow or
sparsely filled interiors, using less material and being lighter to handle.

Scale is an important consideration when printing molecular models. The size of a
tangible molecular model is millions of times the size of the actual molecular
structure that it represents, however it is limited by its convenience to the
human user and by the physical constraints of the 3D printer. The size of actual
molecular structures can range from a small number of atoms in simple chemical
compounds (about 1 nanometer across) to many thousands or millions of atoms in
large molecular assemblies, such as ribosomes and viruses 10s to 100s of
nanometers in diameter. Thus, a single scale for all tangible molecular models
is impractical. Yet, the use of a set of specific scales for molecular models
proves to be beneficial to enable model comparisons and to explore interactions
between them. Using an arbitrary scale for a molecular model may be suitable for
isolated, large sculptural objects, but it limits the utility of hand held
models. We tend to use 40 million times actual size for models made up of
atomically-manipulable components, 20 million times actual size for individual
proteins; 10 million times for protein assemblies with several interacting
protein chains; 5 million times for very large molecular assemblies and viruses;
and 1 million times for larger cellular components and structures. These scales
produce tangible models that can be easily held and manipulated in the hand
(Figure 2).

Figure 2

3D printed molecular models at various scales.
Full color models are made with the powder-based Z Corp printer.
Monochrome models are made with the FDM Stratasys printer

Software for 3D Printed Molecular Models

The most common computer formats accepted by 3D printers are: STL, OBJ, X3D,
Collada or VRML. Many molecular modeling packages now provide output formats
(usually STL or VRML) that are compatible with 3D printers (Table 1). Sending a
file in one of these formats to a 3D printer, however, does not guarantee that
it is physically buildable. As stated above, the file must represent an enclosed
volume, termed a “manifold geometry”. A file with a list of
polygons may have open edges that do not enclose a volume, or polygons may have
surface normals, that are pointing inside rather than outside the object.
Molecular modeling programs do not typically analyze for these, but there are
several programs that can repair such non-manifold geometries, e.g. MeshLab
(http://meshlab.sourceforge.net). While the geometries generated
from these molecular modeling programs may be directly 3D printable, it does not
guarantee that the model is mechanically strong enough to hold together or be
handled. Additionally, one might desire mechanistic features that go beyond the
static shape of the model. For example, one might want to add extra features
such as bolstering or other types of affordances that go beyond the
functionality of the molecular modeling software. For these types of features,
one must use more generic computer-aided design software. Most of the high-end
3D modeling and animation packages now used by medical and scientific
illustrators, such as Maya, 3D Studio Max, Cinema4D, and Blender have sufficient
modeling capabilities to modify input molecular geometries with other
constructed geometries and support operations such as Boolean addition and
subtraction of volumes for the desired finished model geometry. We have produced
a molecular modeling plugin for these 3D modeling and animation packages, called
ePMV (embedded Python Molecular Viewer), that enables the construction of
molecular representations inside these high end codes, eliminating the need to
transfer information between the molecular modeling environment and the more
generic modeling environment.

Examples of 3D Printed Biomolecular Models

The shapes and chemistry of biomolecules dictate their function. 3D printing
enables the representation of these characteristics in a tangible and easily
grasped form. While complex shapes can be produced by most of the current 3D
printers, representing the chemical nature of the molecules can be more
problematic. Color has long been used by chemists to indicate different atom
types (e.g. red oxygen, blue nitrogen, black carbon, etc.). This type of
color-coding has carried through to distinguish other aspects of complex
molecules, such as amino acid type, protein chain identity and electrostatic
potential. Of the 3D printers currently on the market, there are only a few that
can create full color models. These include the Z Corp powder-based printer, and
the Mcor laminated paper printer. While plastic extrusion printers can use
different color filament, and some with multiple heads can incorporate more than
one color into a single object, their ability to mix colors within a layer are
very limited, at best. If the molecular model is comprised and built from
multiple separate parts, then different color plastic can be used to identify
these different parts. Examples of full color molecular models printed on the Z
Corp printer and multiple color assembled plastic models are shown in Figure
1.

3D printing can be used to produce molecular models that demonstrate function, as
well as shape. An example of such a model that we have developed demonstrates
the process of self-assembly of virus capsids. This model is based upon the
atomic resolution structure of the poliovirus (Figure 3).

Figure 3

(a) Two 5-sided poliovirus subunits showing complementary electrostatic
forces between them. (b) Geometry used to make the subunit. (c) Sequence
showing self-assembly of 12 subunits into a complete virus capsid.

The capsid assembles in a hierarchical fashion; wherein five fundamental building
blocks, comprised of four different proteins, first form into a pentagonal
structure, 12 of which then assemble into the intact spherical capsid. We
modeled the last step of this assembly process by printing surface models of the
12 identical pentamers using an FDM plastic printer. In the virus, the edges of
these pentameric subassemblies have complementary electrostatic charges and
shapes that facilitate their assembly. We used magnets, imbedded into the edges
of the model, to mimic this complementarity. In order to place cylindrical
magnets in the proper locations along each edge, we used a generic computer
aided design (CAD) package to Boolean subtract cylindrical holes from our
molecular surface model. Subsequent to printing these models, we placed and
glued the cylindrical magnets, with the proper orientation, into the pre-made
holes, such that the pentamers could attract one another. Placing 12 of these
pentamers into an enclosed container and shaking with the proper energy
demonstrates the process of self-assembly, as the individual pentamers
ultimately find and bind to each other to form a complete spherical capsid
(Figure 3). This model has been used
and tested in a number of educational settings to teach the concept of
self-assembly from random motion.

Many other aspects of biological function can be demonstrated using models
comprised of 3D printed parts. The folding of a protein from a linear polypeptide
chain of amino acids is fundamental to attaining the shape of the functional
molecule. Using the known geometry of the peptide backbone we printed a
Lego-like set of parts, designed to assemble into a chain which can be folded
into a given protein shape. In order to do this, we imbedded magnets into the
peptide unit to mimic the hydrogen bonding that forms the structural backbone
(secondary structure) interactions. We imparted geometric flexibility to the
hydrogen bonding by in situ printing of a ball and socket joint for the hydrogen
bond acceptor to represent its known angular interaction range. Since the
orientation of each amino acid in the chain is related by two rotational angles
(phi and psi) to its two adjacent amino acids, we encoded these angles into the
base (alpha carbon) of each by specifying a complementary fit to each flanking
peptide unit.

The peptide units and the base alpha carbons are strung successively on an
elastic monofilament, such that the tension on the filament drives the
chain into the preferred specific folding configuration. Thus, while the peptide
chain is free to rotate at each amino acid, there is a tangible fit when the
angle of rotation is at the preferred value. Since the major structural motifs
of proteins consist of alpha helices and beta sheets with canonical phi-psi
angles, we have made units of such motifs along with loop structures with no
preferred phi-psi angles that can be snapped together to make a generic protein
folding kit. Because of the accurate protein geometries built into these models,
they demonstrate some of the emergent properties inherent in the building up of
protein structures. We have used these kits in educational settings that range
from high school to graduate school (Figure
4).

Figure 4

We have extended this component-based approach to creating a flexible DNA model
to demonstrate the nature of double helix, base-pair complementarity, templated
replication and other DNA configurations. In this model the four nucleotide
bases are printed in a different color on an FDM plastic printer. Similar to the
polypeptide backbone folding model, the Watson-Crick hydrogen bonds are mimicked
by imbedded magnets. The DNA backbone is created with two kinds of FDM printed
plastic parts, the sugar and the phosphate (white and black, respectively). The
sugar has a snap-bead fitting, designed to mate with any of the nucleotide
bases. The sugar and phosphate units are strung, using elastic monofilament to
create the DNA backbone. Similar to the polypeptide backbone the phosphate has
angles encoded into it that guide preference for the B-form DNA helical
structure. The DNA model components are either strung as five base units to form
a helical half-turn, or as individual nucleoside units, to enable demonstration
reaction of nucleotide triphosphate for base addition via DNA polymerase. The
units have “pop-bead” snap fits at the 5’ and 3’ end
to enable extension of the DNA strands and other DNA structures, such as those
involving strand exchange between two double helices (Figures 5 & 6). This model is currently being tested in
high school biology classes.

Figure 5

Manipulable Flexible DNA Model.3D printed components. The reconfigurable model has sugar,
phosphate and nucleotide components that can be assembled into
arbitrary sequences and lengths of the individual
strands.

Figure 6

Conclusion

As medical science becomes more molecular, the ability to perceive, explore and
understand molecular structures and their interactions become more important for
students, medical practitioners, scientists, and the lay public. Physical models
have a power and presence that is lacking from pictures, animations, and even
interactive computer graphics. The advent of solid 3D printers has popularized the
production of custom physical models and extended their production and application
to models of the unseeable molecular world. The field of 3D printing is still in its
infancy, with new types of printers, materials, and capabilities changing rapidly.
The field of bioprinting biocompatible scaffolds, and even cellular structures, is
one area of great current interest. 3D printing of complete devices that include
power supplies, circuits and actuators is in the near, foreseeable future.

For the purposes of visualization, 3D models can be integrated with the computer
models and molecular information from which they were modeled using the technology
of augmented reality. We have been developing what we term “tangible
molecular interfaces” which combine the manipulation of physical molecular
models with computer visualization and calculation (Figures 7 & 8). As tracking and
computer display technology progresses, the ability to use physical manipulation of
real object will couple seamlessly with the computational environment. We see a
future where of biomedical visualization brings us closer to the molecular world in
which we live. 3D printing will be part of that future.

Figure 7

Augmented reality tangible molecular interface showing manipulation
of two 3D printed physical models of subunits of the enzyme Cu-Zn
superoxide dismutase, augmented on the computer screen with the
electrostatic potential fields that are computed for the two
subunits.

Acknowledgements

The authors acknowledge early input to this work by Jon Huntoon, and the other
members of the Molecular Graphics Laboratory at The Scripps Research Institute.

This work was initiated under National Science Foundation Grant ITR EIA 0121282 to
AJO and NIH Grant R21/R33 GM64340 to AJO, and was continued under NSF Grant
DRL-1108896, and Institute of Education Sciences, U.S. Department of Education Grant
R305A120047 (PI Jodi Davenport).

Biography

Arthur Olson, PhD, is a Professor at The Scripps Research Institute and
director of its Molecular Graphics Laboratory. Olson has pioneered the analysis and
visualization of biological assemblies at scales ranging from atoms to cells. His
laboratory developed AutoDock, the world’s most highly cited ligand-protein
docking code. His latest work in molecular visualization focuses on the development
of novel and intuitive human interfaces for research and education in structural
molecular biology. Olson’s visualizations and animations have reached a broad
audience through public venues such as the Disney EPCOT center, Public television,
and art and science museum exhibits around the world.

Biography

Adam Gardner, BS received his BS in Biology from Minnesota State
University and has worked as an Illustrator and Designer, both in a freelance
capacity and for The Scripps Research Institute (TSRI). Specializing in 3D printing
and computer-based illustration, Adam focuses on the topic of Molecular and
Structural Biology. He runs the Physical Model Service for TSRI and the NBCR NIH
Research Resource. Adam has done work in education and research alike. His work has
been displayed in The Smithsonian Natural History Museum and The San Diego
International Airport, among other venues.

Licensing

The author has chosen to license this content under a Creative Commons Attribution 4.0 International License.